PHILIPPE MEYER

Philippe Meyer

I work in the BioRetroSynth group at the Micalis Institute, a joint research unit of INRAE, AgroParisTech, and the University of Paris-Saclay, located in the Paris area, France.

I am a computational scientist with a background in applied mathematics, working at the interface of cheminformatics, bioinformatics, and artificial intelligence. My research focuses on molecular and pathway design, combining generative models, agentic AI, retrosynthesis and retrobiosynthesis, and hybrid mechanistic–machine learning approaches to explore chemical and biological design spaces. I develop computational methods and scientific software for molecular generation, reaction and pathway prediction, and the modeling of biological systems.

Email: first name dot last name at inrae dot fr

Preprints

  • Engineering growth-coupled metabolic biosensors for disease prognosis and diagnosis using full growth trajectories, Ahavi, P., Hoang, A., Meyer, P., Epaulard, O., Le Gouellec, A., Faulon, J.-L., in reviewing, 2026. Link, Code
  • Contrastive-to-self-supervised: a two-stage framework for script similarity learning, Roman, C., Meyer, P., in reviewing, 2026. Link

Publications

  • Representing chemical and enzymatic reactions in fingerprint space for applicability filtering and classification, Meyer, P., Duigou, T., Gricourt, G., Faulon, J.-L., to appear in Journal of Cheminformatics, 2026. Link, Code
  • An agentic retrobiosynthesis framework with learned frontier selection, Meyer, P., Gricourt, G., Duigou, T., Hérisson J., Faulon, J.-L., accepted at the NeurIPS 2026 Workshop on ML4Molecules: Agentic Systems for Molecular Sciences, 2026. Link
  • A quantitative visual taxonomy of worldwide writing systems, Meyer, P., Roman, C., to appear in Proceedings of the 40th Conference on Neural Information Processing Systems (NeurIPS), 2026.
  • End-to-end mapping of membrane transport from chemical structure to microorganisms, Gricourt, G., Duigou, T., Meyer, P., Faulon, J.-L., to appear in Communications Chemistry, 2026. Link, Code
  • Living bacterial reservoir computers for information processing and sensing, Ahavi, P., Hoang, A., Meyer, P., Berthier, S., Fiorini, F., Castelli, F., Epaulard, O., Le Gouellec, A., Faulon, J.-L., Cell Systems, 2026. Link, Code, News (INRAE), News (UPSaclay)
  • RetroRules 2026: an expanded database combining biochemical and organic reaction templates for pathway discovery, Duigou, T., Meyer, P., Faulon, J.-L., Nucleic Acids Research, 2026. Link, API
  • Reverse engineering molecules from fingerprints through deterministic enumeration and generative models, Meyer, P., Duigou, T., Gricourt, G., Faulon, J.-L., Journal of Cheminformatics, 17 (1), 157, 2025. Link, Poster, Code, News (UPSaclay), Application
  • Artificial intelligence methods and models for retro-biosynthesis: a scoping review, Gricourt, G., Meyer, P., Duigou, T., Faulon, J.-L., ACS Synthetic Biology, 13 (8), 2276–2294, 2024. Link, Poster
  • Analysis of glyph and writing system similarities using siamese neural networks, Roman, C., Meyer, P., Proceedings of the Third Workshop on Language Technologies for Historical and Ancient Languages (LT4HALA) @ LREC-COLING-2024, 98–104, 2024. Link, Poster, Code, 3D view
  • Human body shapes anomaly detection and classification using persistent homology, de Rose, S., Meyer, P., Bertrand, F., Machine Learning for Pattern Recognition, Algorithms, 16 (3), 161, 2023. Link, Code
  • Missing body measurements prediction in fashion industry: a comparative approach, Meyer, P., Birregah, B., Beauseroy, P., Grall, E., Lauxerrois, A., Fashion and Textiles, 10 (1), 37, 2023. Link
  • Geometric properties of special orthogonal representations associated to exceptional Lie superalgebras, Meyer, P., Reviews in Mathematical Physics, 35 (10), 2350026, 2023. Link
  • Symplectic Dirac operators for Lie algebras and graded Hecke algebras, Ciubotaru, D., de Martino, M., Meyer, P., Transformation Groups, 28 (4), 1447–1475, 2023. Link
  • Cubic Dirac operators and the strange Freudenthal–de Vries formula for colour Lie algebras, Meyer, P., Transformation Groups, 27 (4), 1307–1336, 2022. Link
  • Involutions of sl(2,k) and non-split, three-dimensional simple Lie algebras, Meyer, P., Journal of Algebra and Its Applications, 22 (6), 2350139, 2022. Link
  • The Kostant invariant and special ϵ-orthogonal representations for ϵ-quadratic colour Lie algebras, Meyer, P., Journal of Algebra, 572, 337–380, 2021. Link
  • Classification of finite-dimensional Lie superalgebras whose even part is a three-dimensional simple Lie algebra over a field of characteristic not 2 or 3, Meyer, P., Communications in Algebra, 47 (11), 4654–4675, 2019. Link

Codes

List of the codes I have developed: Python packages and repositories supporting my work, in cheminformatics, synthetic biology and beyond.

Talks

  • From Molecules to Metabolic Pathways: Computational Approaches for Retrobiosynthesis and Bioproduction, Séminaire Micalis, Jouy-en-Josas, 11.09.2026.
  • Vectorized Chemical Reactions and Fingerprint Reverse Engineering for Molecular Design, 19th GCC - German Conference on Cheminformatics, Bad Soden am Taunus (Germany), 10.11.2026.

    • Past talks

Workshops

  • Co-organisor of the Journée Outils numériques de l’axe 4 du PEPR B-BEST, Institut des Systèmes Complexes, Paris, 18.11.2025. Flyer
  • Co-organisor of the AI Methods and Models for (Bio)Catalysis and Synthetic Biology Workshop, pre BioSynSys 2024, Montpellier, 05.06.2024. Link, Booklet

Documents

  • Représentations associées à des graduations d'algèbres de Lie et d'algèbres de Lie colorées, Meyer, P., PhD thesis, Université de Strasbourg, 2019. Link, Poster

Links

       Google Scholar  ·  GitHub  ·  ResearchGate  ·  ORCID  ·  LinkedIn

Other

I preserve and share the work of my grandfather Pierre Meyer on traces of a prehistoric civilisation in Alsace (6000–2000 BC), characterised by a Great Goddess cult. YouTube, Book (Amazon), Book (Ebay)

I also have an interest in Rennes-le-Château, its local history and the enduring mystery surrounding the alleged treasure associated with the village. I occasionally write about related historical subjects. Article